Application for data recovery on DOS works slow with USB

We have an application written in C ( using DJGPP) for data backup & recovery & is used in DOS environment. Its somewhat similar in function to Ghost but a simpler functionality. It works fine on PXE but when running on USB it takes lot of time.
We are using simple fread & fwrite calls to read/write data.

We tried taking the USBASPI driver from one of links mentioned in one forum here, just to see that if driver takes up these calls & makes things faster and execution time reduces.
But the USBASPI driver hangs in scanning phase.

Please suggest how we can improve this time. Any help would be highly appreciated.

Regards,
SK